Index

_

__init__() (chemtorch.components.data_pipeline.column_mapper.column_filter_rename.ColumnFilterAndRename method) (chemtorch.components.data_pipeline.data_source.pre_split_csv_source.PreSplitCSVSource method) (chemtorch.components.data_pipeline.data_source.single_csv_source.SingleCSVSource method) (chemtorch.components.data_pipeline.data_splitter.data_splitter_base.DataSplitterBase method) (chemtorch.components.data_pipeline.data_splitter.index_splitter.IndexSplitter method) (chemtorch.components.data_pipeline.data_splitter.ratio_splitter.RatioSplitter method) (chemtorch.components.data_pipeline.data_splitter.reaction_core_splitter.ReactionCoreSplitter method) (chemtorch.components.data_pipeline.data_splitter.scaffold_splitter.ScaffoldSplitter method) (chemtorch.components.data_pipeline.data_splitter.size_splitter.SizeSplitter method) (chemtorch.components.data_pipeline.data_splitter.target_splitter.TargetSplitter method) (chemtorch.components.data_pipeline.simple_data_pipeline.SimpleDataPipeline method) (chemtorch.components.layer.gnn_layer.dmpnn_stack.DMPNNStack method) (chemtorch.components.layer.gnn_layer.dmpnn_stack.EdgeToNodeEmbedding method) (chemtorch.components.layer.layer_stack.LayerStack method) (chemtorch.components.model.dimenet.BesselBasisLayer method) (chemtorch.components.model.dimenet.DimeNet method) (chemtorch.components.model.dimenet.DimeNetPlusPlus method) (chemtorch.components.model.dimenet.EmbeddingBlock method) (chemtorch.components.model.dimenet.Envelope method) (chemtorch.components.model.dimenet.InteractionBlock method) (chemtorch.components.model.dimenet.InteractionPPBlock method) (chemtorch.components.model.dimenet.OutputBlock method) (chemtorch.components.model.dimenet.OutputPPBlock method) (chemtorch.components.model.dimenet.ResidualLayer method) (chemtorch.components.model.dimenet.SphericalBasisLayer method) (chemtorch.components.model.gnn.gnn.GNN method) (chemtorch.components.model.han.HAN method) (chemtorch.components.model.mlp.MLP method) (chemtorch.components.representation.fingerprint.drfp.DRFP method) (chemtorch.components.representation.graph.cgr.CGR method) (chemtorch.components.representation.graph.reaction_3d_graph.Reaction3DData method) (chemtorch.components.representation.graph.reaction_3d_graph.Reaction3DGraph method) (chemtorch.core.data_module.DataModule method) (chemtorch.core.dataset_base.DatasetBase method) (chemtorch.core.property_system.DatasetProperty method) (chemtorch.core.routine.regression_routine.RegressionRoutine method) (chemtorch.core.routine.supervised_routine.SupervisedRoutine method) (chemtorch.core.scheduler.cosine_with_warmup_lr.CosineWithWarmupLR method) (chemtorch.core.scheduler.sequential_lr_wrapper.SequentialLRWrapper method) (chemtorch.utils.callable_compose.CallableCompose method) (chemtorch.utils.standardizer.Standardizer method) (chemtorch.utils.types.DataLoaderFactoryProtocol method) (chemtorch.utils.types.DataSplit method) (chemtorch.utils.types.RoutineFactoryProtocol method)

A

AbstractAugmentation (class in chemtorch.components.augmentation.abstract_augmentation) AbstractColumnMapper (class in chemtorch.components.data_pipeline.column_mapper.abstract_column_mapper) AbstractDataSource (class in chemtorch.components.data_pipeline.data_source.abstract_data_source)

AbstractDataSplitter (class in chemtorch.components.data_pipeline.data_splitter.abstract_data_splitter) AbstractRepresentation (class in chemtorch.components.representation.abstract_representation) AbstractTransform (class in chemtorch.components.transform.abstract_transform) AtomOriginType (class in chemtorch.utils.atom_mapping)

B

batch (chemtorch.components.model.dimenet.DimeNet attribute) (chemtorch.components.model.dimenet.DimeReaction attribute)

BesselBasisLayer (class in chemtorch.components.model.dimenet) bondtypes() (in module chemtorch.utils.reaction_utils)

C

CallableCompose (class in chemtorch.utils.callable_compose) CGR (class in chemtorch.components.representation.graph.cgr) chemtorch.components.augmentation.abstract_augmentation module chemtorch.components.data_pipeline.column_mapper.abstract_column_mapper module chemtorch.components.data_pipeline.column_mapper.column_filter_rename module chemtorch.components.data_pipeline.data_source.abstract_data_source module chemtorch.components.data_pipeline.data_source.pre_split_csv_source module chemtorch.components.data_pipeline.data_source.single_csv_source module chemtorch.components.data_pipeline.data_splitter.abstract_data_splitter module chemtorch.components.data_pipeline.data_splitter.data_splitter_base module chemtorch.components.data_pipeline.data_splitter.index_splitter module chemtorch.components.data_pipeline.data_splitter.ratio_splitter module chemtorch.components.data_pipeline.data_splitter.reaction_core_splitter module chemtorch.components.data_pipeline.data_splitter.scaffold_splitter module chemtorch.components.data_pipeline.data_splitter.size_splitter module chemtorch.components.data_pipeline.data_splitter.target_splitter module chemtorch.components.data_pipeline.simple_data_pipeline module chemtorch.components.layer.gnn_layer.dmpnn_stack module chemtorch.components.layer.layer_stack module chemtorch.components.model.dimenet module chemtorch.components.model.gnn.encoder module chemtorch.components.model.gnn.gnn module chemtorch.components.model.gnn.pool module chemtorch.components.model.han module chemtorch.components.model.mlp module chemtorch.components.representation.abstract_representation module chemtorch.components.representation.fingerprint.drfp module chemtorch.components.representation.graph.cgr module chemtorch.components.representation.graph.reaction_3d_graph module

chemtorch.components.transform.abstract_transform module chemtorch.components.transform.graph_transform module chemtorch.core.data_module module chemtorch.core.dataset_base module chemtorch.core.property_system module chemtorch.core.routine.regression_routine module chemtorch.core.routine.supervised_routine module chemtorch.core.scheduler.cosine_with_warmup_lr module chemtorch.core.scheduler.graphgps_cosine_with_warmup_lr module chemtorch.core.scheduler.sequential_lr_wrapper module chemtorch.utils.atom_mapping module chemtorch.utils.callable_compose module chemtorch.utils.cli module chemtorch.utils.decorators.enforce_base_init module chemtorch.utils.hydra module chemtorch.utils.misc module chemtorch.utils.reaction_utils module chemtorch.utils.standardizer module chemtorch.utils.types module cli_chemtorch_logo() (in module chemtorch.utils.cli) ColumnFilterAndRename (class in chemtorch.components.data_pipeline.column_mapper.column_filter_rename) compose() (chemtorch.utils.callable_compose.CallableCompose static method) compute() (chemtorch.core.property_system.DatasetProperty method) (chemtorch.core.property_system.DegreeStatistics method) (chemtorch.core.property_system.FingerprintLength method) (chemtorch.core.property_system.LabelMean method) (chemtorch.core.property_system.LabelStd method) (chemtorch.core.property_system.NumEdgeFeatures method) (chemtorch.core.property_system.NumNodeFeatures method) (chemtorch.core.property_system.PrecomputeTime method) (chemtorch.core.property_system.VocabSize method) compute_property_with_dataset_handling() (in module chemtorch.core.property_system) configure_optimizers() (chemtorch.core.routine.supervised_routine.SupervisedRoutine method) construct() (chemtorch.components.representation.abstract_representation.AbstractRepresentation method) (chemtorch.components.representation.fingerprint.drfp.DRFP method) (chemtorch.components.representation.graph.cgr.CGR method) (chemtorch.components.representation.graph.reaction_3d_graph.Reaction3DGraph method) CosineWithWarmupLR (class in chemtorch.core.scheduler.cosine_with_warmup_lr)

D

DataLoaderFactoryProtocol (class in chemtorch.utils.types) DataModule (class in chemtorch.core.data_module) DatasetBase (class in chemtorch.core.dataset_base) DatasetProperty (class in chemtorch.core.property_system) DataSplit (class in chemtorch.utils.types) DataSplitterBase (class in chemtorch.components.data_pipeline.data_splitter.data_splitter_base) DegreeStatistics (class in chemtorch.core.property_system) destandardize() (chemtorch.utils.standardizer.Standardizer method)

DimeNet (class in chemtorch.components.model.dimenet) DimeNetPlusPlus (class in chemtorch.components.model.dimenet) DimeReaction (class in chemtorch.components.model.dimenet) DMPNNStack (class in chemtorch.components.layer.gnn_layer.dmpnn_stack) DRFP (class in chemtorch.components.representation.fingerprint.drfp) DRFPUtil (class in chemtorch.components.representation.fingerprint.drfp) DUMMY (chemtorch.utils.atom_mapping.AtomOriginType attribute) (chemtorch.utils.atom_mapping.EdgeOriginType attribute)

E

EdgeOriginType (class in chemtorch.utils.atom_mapping) EdgeToNodeEmbedding (class in chemtorch.components.layer.gnn_layer.dmpnn_stack) embed() (chemtorch.components.model.dimenet.DimeNet method)

EmbeddingBlock (class in chemtorch.components.model.dimenet) encode() (chemtorch.components.representation.fingerprint.drfp.DRFPUtil static method) enforce_base_init() (in module chemtorch.utils.decorators.enforce_base_init) Envelope (class in chemtorch.components.model.dimenet)

F

filter_config_by_signature() (in module chemtorch.utils.hydra) FingerprintLength (class in chemtorch.core.property_system) fold() (chemtorch.components.representation.fingerprint.drfp.DRFPUtil static method) forward() (chemtorch.components.layer.gnn_layer.dmpnn_stack.DMPNNStack method) (chemtorch.components.layer.gnn_layer.dmpnn_stack.EdgeToNodeEmbedding method) (chemtorch.components.layer.layer_stack.LayerStack method) (chemtorch.components.model.dimenet.BesselBasisLayer method) (chemtorch.components.model.dimenet.DimeNet method) (chemtorch.components.model.dimenet.DimeReaction method) (chemtorch.components.model.dimenet.EmbeddingBlock method) (chemtorch.components.model.dimenet.Envelope method) (chemtorch.components.model.dimenet.InteractionBlock method) (chemtorch.components.model.dimenet.InteractionPPBlock method) (chemtorch.components.model.dimenet.OutputBlock method) (chemtorch.components.model.dimenet.OutputPPBlock method) (chemtorch.components.model.dimenet.ResidualLayer method) (chemtorch.components.model.dimenet.SphericalBasisLayer method) (chemtorch.components.model.gnn.gnn.GNN method) (chemtorch.components.model.han.HAN method) (chemtorch.components.model.mlp.MLP method) (chemtorch.core.routine.regression_routine.RegressionRoutine method) (chemtorch.core.routine.supervised_routine.SupervisedRoutine method)

G

get_atom_index_by_mapnum() (in module chemtorch.utils.reaction_utils) get_cosine_scheduler_with_warmup() (in module chemtorch.core.scheduler.graphgps_cosine_with_warmup_lr) get_dataset() (chemtorch.core.data_module.DataModule method) get_dataset_names() (chemtorch.core.data_module.DataModule method)

get_labels() (chemtorch.core.dataset_base.DatasetBase method) get_last_lr() (chemtorch.core.scheduler.cosine_with_warmup_lr.CosineWithWarmupLR method) get_num_workers() (in module chemtorch.utils.hydra) get_reaction_core() (in module chemtorch.utils.reaction_utils) GNN (class in chemtorch.components.model.gnn.gnn)

H

HAN (class in chemtorch.components.model.han)

handle_prediction_saving() (in module chemtorch.utils.misc) hash() (chemtorch.components.representation.fingerprint.drfp.DRFPUtil static method)

I

IndexSplitter (class in chemtorch.components.data_pipeline.data_splitter.index_splitter) InteractionBlock (class in chemtorch.components.model.dimenet)

InteractionPPBlock (class in chemtorch.components.model.dimenet) internal_encode() (chemtorch.components.representation.fingerprint.drfp.DRFPUtil static method)

L

LabelMean (class in chemtorch.core.property_system) LabelStd (class in chemtorch.core.property_system) LayerStack (class in chemtorch.components.layer.layer_stack)

load() (chemtorch.components.data_pipeline.data_source.abstract_data_source.AbstractDataSource method) (chemtorch.components.data_pipeline.data_source.pre_split_csv_source.PreSplitCSVSource method) (chemtorch.components.data_pipeline.data_source.single_csv_source.SingleCSVSource method) load_state_dict() (chemtorch.core.scheduler.cosine_with_warmup_lr.CosineWithWarmupLR method)

M

make_dataloader() (chemtorch.core.data_module.DataModule method) make_mol() (in module chemtorch.utils.atom_mapping) map_reac_to_prod() (in module chemtorch.utils.atom_mapping) maybe_get_test_dataloader_idx_to_suffix() (chemtorch.core.data_module.DataModule method) MLP (class in chemtorch.components.model.mlp) module chemtorch.components.augmentation.abstract_augmentation chemtorch.components.data_pipeline.column_mapper.abstract_column_mapper chemtorch.components.data_pipeline.column_mapper.column_filter_rename chemtorch.components.data_pipeline.data_source.abstract_data_source chemtorch.components.data_pipeline.data_source.pre_split_csv_source chemtorch.components.data_pipeline.data_source.single_csv_source chemtorch.components.data_pipeline.data_splitter.abstract_data_splitter chemtorch.components.data_pipeline.data_splitter.data_splitter_base chemtorch.components.data_pipeline.data_splitter.index_splitter chemtorch.components.data_pipeline.data_splitter.ratio_splitter chemtorch.components.data_pipeline.data_splitter.reaction_core_splitter chemtorch.components.data_pipeline.data_splitter.scaffold_splitter chemtorch.components.data_pipeline.data_splitter.size_splitter chemtorch.components.data_pipeline.data_splitter.target_splitter chemtorch.components.data_pipeline.simple_data_pipeline chemtorch.components.layer.gnn_layer.dmpnn_stack chemtorch.components.layer.layer_stack chemtorch.components.model.dimenet chemtorch.components.model.gnn.encoder chemtorch.components.model.gnn.gnn chemtorch.components.model.gnn.pool chemtorch.components.model.han chemtorch.components.model.mlp chemtorch.components.representation.abstract_representation chemtorch.components.representation.fingerprint.drfp chemtorch.components.representation.graph.cgr chemtorch.components.representation.graph.reaction_3d_graph chemtorch.components.transform.abstract_transform chemtorch.components.transform.graph_transform chemtorch.core.data_module chemtorch.core.dataset_base chemtorch.core.property_system chemtorch.core.routine.regression_routine chemtorch.core.routine.supervised_routine chemtorch.core.scheduler.cosine_with_warmup_lr chemtorch.core.scheduler.graphgps_cosine_with_warmup_lr chemtorch.core.scheduler.sequential_lr_wrapper chemtorch.utils.atom_mapping chemtorch.utils.callable_compose chemtorch.utils.cli chemtorch.utils.decorators.enforce_base_init chemtorch.utils.hydra chemtorch.utils.misc chemtorch.utils.reaction_utils chemtorch.utils.standardizer chemtorch.utils.types

N

neighbors() (in module chemtorch.utils.reaction_utils) neighbors_and_bondtypes() (in module chemtorch.utils.reaction_utils)

NumEdgeFeatures (class in chemtorch.core.property_system) NumNodeFeatures (class in chemtorch.core.property_system)

O

on_load_checkpoint() (chemtorch.core.routine.regression_routine.RegressionRoutine method) on_save_checkpoint() (chemtorch.core.routine.regression_routine.RegressionRoutine method)

order_config_by_signature() (in module chemtorch.utils.hydra) OutputBlock (class in chemtorch.components.model.dimenet) OutputPPBlock (class in chemtorch.components.model.dimenet)

P

pos (chemtorch.components.model.dimenet.DimeNet attribute) pos_r (chemtorch.components.model.dimenet.DimeReaction attribute) (chemtorch.components.representation.graph.reaction_3d_graph.Reaction3DData attribute), [1] pos_ts (chemtorch.components.model.dimenet.DimeReaction attribute) (chemtorch.components.representation.graph.reaction_3d_graph.Reaction3DData attribute), [1] PrecomputeTime (class in chemtorch.core.property_system)

predict_dataloader() (chemtorch.core.data_module.DataModule method) predict_step() (chemtorch.core.routine.regression_routine.RegressionRoutine method) (chemtorch.core.routine.supervised_routine.SupervisedRoutine method) PreSplitCSVSource (class in chemtorch.components.data_pipeline.data_source.pre_split_csv_source) PRODUCT (chemtorch.utils.atom_mapping.AtomOriginType attribute) (chemtorch.utils.atom_mapping.EdgeOriginType attribute)

R

RatioSplitter (class in chemtorch.components.data_pipeline.data_splitter.ratio_splitter) REACTANT (chemtorch.utils.atom_mapping.AtomOriginType attribute) (chemtorch.utils.atom_mapping.EdgeOriginType attribute) REACTANT_PRODUCT (chemtorch.utils.atom_mapping.AtomOriginType attribute) (chemtorch.utils.atom_mapping.EdgeOriginType attribute) Reaction3DData (class in chemtorch.components.representation.graph.reaction_3d_graph) Reaction3DGraph (class in chemtorch.components.representation.graph.reaction_3d_graph) ReactionCoreSplitter (class in chemtorch.components.data_pipeline.data_splitter.reaction_core_splitter) read_xyz() (in module chemtorch.components.representation.graph.reaction_3d_graph) RegressionRoutine (class in chemtorch.core.routine.regression_routine) remove_atom_mapping() (in module chemtorch.utils.atom_mapping) remove_atoms_from_rxn() (in module chemtorch.utils.reaction_utils)

reset_parameters() (chemtorch.components.model.dimenet.BesselBasisLayer method) (chemtorch.components.model.dimenet.DimeNet method) (chemtorch.components.model.dimenet.EmbeddingBlock method) (chemtorch.components.model.dimenet.InteractionBlock method) (chemtorch.components.model.dimenet.InteractionPPBlock method) (chemtorch.components.model.dimenet.OutputBlock method) (chemtorch.components.model.dimenet.OutputPPBlock method) (chemtorch.components.model.dimenet.ResidualLayer method) ResidualLayer (class in chemtorch.components.model.dimenet) resolve_sources() (in module chemtorch.core.property_system) resolve_target() (in module chemtorch.utils.hydra) RoutineFactoryProtocol (class in chemtorch.utils.types)

S

safe_instantiate() (in module chemtorch.utils.hydra) save_predictions() (in module chemtorch.utils.misc) ScaffoldSplitter (class in chemtorch.components.data_pipeline.data_splitter.scaffold_splitter) SequentialLRWrapper (class in chemtorch.core.scheduler.sequential_lr_wrapper) setup() (chemtorch.core.routine.supervised_routine.SupervisedRoutine method) shingling_from_mol() (chemtorch.components.representation.fingerprint.drfp.DRFPUtil static method) SimpleDataPipeline (class in chemtorch.components.data_pipeline.simple_data_pipeline) SingleCSVSource (class in chemtorch.components.data_pipeline.data_source.single_csv_source) SizeSplitter (class in chemtorch.components.data_pipeline.data_splitter.size_splitter)

smarts2smarts() (in module chemtorch.utils.reaction_utils) smiles2smiles() (in module chemtorch.utils.reaction_utils) SphericalBasisLayer (class in chemtorch.components.model.dimenet) standardize() (chemtorch.utils.standardizer.Standardizer method) Standardizer (class in chemtorch.utils.standardizer) state_dict() (chemtorch.core.scheduler.cosine_with_warmup_lr.CosineWithWarmupLR method) step() (chemtorch.core.scheduler.cosine_with_warmup_lr.CosineWithWarmupLR method) SupervisedRoutine (class in chemtorch.core.routine.supervised_routine) symbols_to_atomic_numbers() (in module chemtorch.components.representation.graph.reaction_3d_graph)

T

TargetSplitter (class in chemtorch.components.data_pipeline.data_splitter.target_splitter) test_dataloader() (chemtorch.core.data_module.DataModule method) test_step() (chemtorch.core.routine.supervised_routine.SupervisedRoutine method)

to_dict() (chemtorch.utils.types.DataSplit method) train_dataloader() (chemtorch.core.data_module.DataModule method) training_step() (chemtorch.core.routine.supervised_routine.SupervisedRoutine method) triplets() (in module chemtorch.components.model.dimenet)

U

unmap_smarts() (in module chemtorch.utils.reaction_utils) unmap_smiles() (in module chemtorch.utils.reaction_utils)

url (chemtorch.components.model.dimenet.DimeNet attribute) (chemtorch.components.model.dimenet.DimeNetPlusPlus attribute)

V

val_dataloader() (chemtorch.core.data_module.DataModule method) validate() (chemtorch.utils.standardizer.Standardizer static method)

validation_step() (chemtorch.core.routine.supervised_routine.SupervisedRoutine method) VocabSize (class in chemtorch.core.property_system)

Z

z_r (chemtorch.components.representation.graph.reaction_3d_graph.Reaction3DData attribute), [1]

z_ts (chemtorch.components.model.dimenet.DimeReaction attribute) (chemtorch.components.representation.graph.reaction_3d_graph.Reaction3DData attribute), [1]